PAM p.Asp649=
c.1947T>C · rs374784351 · VCV745814
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.245%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.289 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.1 | GERP -5 |
| Overall | ||
| CADD | 6.44 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.245%
East Asian · 110/44,882 alleles
Filtering AF
0.208%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.194%
Overall
0.0116%
187/1,614,104 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.245% | 408 |
| Remaining individualsnot grpmax-eligible | 0.0992% | 1,008 |
| Admixed American | 0.02% | 4,999 |
| South Asian | 0.00329% | 30,359 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- PAM
- Protein
- p.Asp649=
- Coding
- c.1947T>C
- MANE Select
- NM_015057 · reported on NM_001177306
- dbSNP
- rs374784351
- Type
- single nucleotide variant
- Location
- chr5:103006944 (GRCh38)
Similar variants
- MYCBP2 p.Asp4042Val Uncertain significance ★★ same type
- MYCBP2 p.Asp4087Asn Uncertain significance ★★ same type
- MYCBP2 p.Gly877Ala Uncertain significance ★★ ⚠ same type
- MYCBP2 p.His2087Leu Uncertain significance ★★ ⚠ same type
- MYCBP2 p.Leu3349Phe Uncertain significance ★★ ⚠ same type
- MYCBP2 p.Lys2309Ter Uncertain significance ★★ same type
- MYCBP2 p.Phe1319Leu Uncertain significance ★★ same type
- MYCBP2 p.Tyr962Cys Uncertain significance ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/pam-p-asp649 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown